From: pschloss <pschloss>
Date: Fri, 11 Feb 2011 12:32:21 +0000 (+0000)
Subject: shhh.seqs and trim.flows modifications.
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=2a99ff8ba22dda9d0c1b125e5c9ff91e23ed6879

shhh.seqs and trim.flows modifications.
---

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 7768fa7..14eee60 100644
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -171,7 +171,15 @@ ShhherCommand::ShhherCommand(string option) {
 				m->mothurOutEndLine();
 				abort = true; 
 			}
-			else if (flowFileName == "not open" || flowFilesFileName == "not open") { abort = true; }	
+			else if (flowFileName == "not open" || flowFilesFileName == "not open") { abort = true; }
+			
+			if(flowFileName != "not found"){	compositeFASTAFileName = "";	}
+			else{
+				compositeFASTAFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "pn.fasta";
+				ofstream temp;
+				m->openOutputFile(compositeFASTAFileName, temp);
+				temp.close();
+			}
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	
@@ -326,9 +334,7 @@ int ShhherCommand::execute(){
 				
 				cout << "\nClustering flowgrams..." << endl;
 				string listFileName = cluster(distFileName, namesFileName);
-	//			string listFileName = "PriestPot_C7.pn.list";
-	//			string listFileName = "test.mock_rep3.v69.pn.list";
-			
+
 				getOTUData(listFileName);
 				initPyroCluster();
 
@@ -1992,7 +1998,6 @@ void ShhherCommand::writeQualities(vector<int> otuCounts){
 
 void ShhherCommand::writeSequences(vector<int> otuCounts){
 	try {
-		
 		string bases = "TACG";
 		
 		string fastaFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.fasta";
@@ -2018,6 +2023,10 @@ void ShhherCommand::writeSequences(vector<int> otuCounts){
 			}
 		}
 		fastaFile.close();
+		
+		if(compositeFASTAFileName != ""){
+			m->appendFiles(fastaFileName, compositeFASTAFileName);
+		}
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ShhherCommand", "writeSequences");
diff --git a/shhhercommand.h b/shhhercommand.h
index 650bf8c..9e50824 100644
--- a/shhhercommand.h
+++ b/shhhercommand.h
@@ -33,7 +33,8 @@ private:
 	int abort;
 	map<string, vector<string> > outputTypes;
 	
-	string outputDir, flowFileName, flowFilesFileName, lookupFileName;
+	string outputDir, flowFileName, flowFilesFileName, lookupFileName, compositeFASTAFileName;
+
 	int processors, maxIters;
 	float cutoff, sigma, minDelta;
 	
diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 960a59d..8184327 100644
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -221,10 +221,10 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
 			convert(temp, tdiffs);
 			if(tdiffs == 0){	tdiffs = bdiffs + pdiffs;	}
 			
-			temp = validParameter.validFile(parameters, "allfiles", false);		if (temp == "not found") { temp = "T";		}
+			temp = validParameter.validFile(parameters, "allfiles", false);		if (temp == "not found"){ temp = "T";		}
 			allFiles = m->isTrue(temp);
 			
-			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found") { temp = "1"; }
+			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){ temp = "1";		}
 			convert(temp, processors); 
 			
 			if(oligoFileName == ""){	allFiles = 0;		}
@@ -322,6 +322,7 @@ int TrimFlowsCommand::execute(){
 			output.close();
 		}
 		outputTypes["flow.files"].push_back(flowFilesFileName);
+		outputNames.push_back(flowFileName);
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -431,15 +432,13 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
 				if(fasta)	{	currSeq.printSequence(fastaFile);	}
 				
 				if(allFiles){
-//					string fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + barcodePrimerCombos[barcodeIndex][primerIndex] + ".flow";
 					ofstream output;
 					m->openOutputFileAppend(barcodePrimerComboFileNames[barcodeIndex][primerIndex], output);
 					output.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
 					
 					flowData.printFlows(output);
 					output.close();
-				}
-				
+				}				
 			}
 			else{
 				flowData.printFlows(scrapFlowFile, trashCode);